Base-stacking and base-pairing contributions into thermal stability of the DNA double helix

By Peter Yakovchuk, E. Protozanova, Maxim D. Frank-Kamenetskii. Nucleic Acids Research, 2006

924 citations recorded by the source corpus.

Two factors are mainly responsible for the stability of the DNA double helix: base pairing between complementary strands and stacking between adjacent bases. By studying DNA molecules with solitary nicks and gaps we measure temperature and salt dependence of the stacking free energy of the DNA double helix. For the first time, DNA stacking parameters are obtained directly (without extrapolation) for temperatures from below room temperature to close to melting temperature. We also obtain DNA stacking parameters for different salt concentrations ranging from 15 to 100 mM Na+. From stacking parameters of individual contacts, we calculate base-stacking contribution to the stability of A•T- and G•C-containing DNA polymers. We find that temperature and salt dependences of the stacking term fully determine the temperature and the salt dependence of DNA stability parameters. For all temperatures and salt concentrations employed in present study, base-stacking is the main stabilizing factor in the DNA double helix. A•T pairing is always destabilizing and G•C pairing contributes almost no stabilization. Base-stacking interaction dominates not only in the duplex overall stability but also significantly contributes into the dependence of the duplex stability on its sequence.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/976b57f8b3358051791cc4701855ce6bd758272e

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Citations in the corpus

Protein and DNA Sequence Determinants of Thermophilic Adaptation (2006, background): “GC pairs in the double helix have stronger base-pairing interactions than AT pairs [21], while purines, A and G, yield a low energy of stacking [27,28,38].”
Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions (2014, neutral): “, AA/TT, AT and TA) [24–27].”
Sequence-Dependent Basepair Opening in DNA Double Helix (2006, methodology): “our treatment upon Protozanova et al. (37) and Yakovchuk et al. ( 38 ); each stacking contributes, roughly, between 0 and � 2.5 kcal/mol, whereas basepairing contributes very little.”
Chemistry, structure and function of approved oligonucleotide therapeutics (2023, background): “Stacking is ultimately more important for pairing stability than H-bonds; the latter of course provide specificity (92,93).”
An Analytical and Computational Infrared Spectroscopic Review of Vibrational Modes in Nucleic Acids (2016, background): “Two forces are mainly responsible for stabilization of DNA double helix: the first force is provided by hydrogen bonds of nucleotides and the second force is provided by base–stacking interactions between aromatic nucleobases [29].”